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The Mars Orbital staging grounds became the rendezvous of most reinforcements from deep space.

By the end of the Second Robotech War, a number of reinforcements from hyperspace had arrived from the Robotech Expeditionary Force (REF). With the United Earth Forces (UEF) in disarray, the expeditionary flotilla, commanded by Commodore Benson and accomapnied by the legendary Col. Jonathan Wolfe, step in to mitigate further disaster. The UEF are reorganized under a restructured command, with retired war veteran Maistroff being named Supreme Commander. Together, they begin rebuilding Earth's shattered defenses while attempting to restore order to the planet.

Within months, the Invid arrive via great pillars of light. The combined defense forces, weary from constant battle with the remaining Robotech Masters are no match for the battle hungry Invid, a race of protoplasmic creatures, who responded to a large buildup of protoculture on Earth directly attributable to the Second Robotech War. Their supreme ruler, the Invid Regess, brought her entire civilization to Earth in hopes of cultivating protoculture, a multipurpose energy source and food stuff, from the Invid Flower of Life.

Bye bye Earth.

In desperation, the surviving members of the United Earth Government and other valuable personnel evacuate the now overrun Earth. Those unlucky to flee are forced into hiding or surrender to these newest invaders. The Invid control near Earthspace and much of the planet's surface, turning it into a slave colony to harvest the Flower of Life and process protoculture.

The Invid operate from a series of hives positioned worldwide, with the main hive cluster located over the North American Great Lakes, centered in Michigan and designated as Reflex Point, . While conducting enlightened evolutionary experiments to find the ultimate lifeform, the Regess also performed cybernetic research and gruesome vivisection on captured human specimens. The Invid also search for armed resistance and active combat mecha, providing Invid collaborators and pacifists with the means to betray their fellow man.

Three years later, another Mars Base fleet is sent to spearhead another operation to retake humanities' ancestral home planet. The Second Reclamation Force, having learnt from their mistakes in the past, is armed with a full complement of the space force's most advanced Veritech mecha in their arsenal, the Alpha Fighter and Beta Fighter. Their initial encounter with the Invid defense force proceeds as well as expected. The powerful Veritechs fire volly after volly of missiles against swarms of Invid fighters. The battle grew steadily more desperate as the Invid continued sending wave after wave of reinforcements from Reflex Point. Before the Terran forces realized what was happening, they were hopelessly overwhelmed. What followed was a slaughter. Invid troopers began slamming themselves into capital ships. The surviving fleet commanders panicked and attempted to enter Earth counter to its rotation, resulting in many cruisers burning up during atmospheric entry. In the end, much of the reclamation force was wiped out before they could even reach Earth's surface. The handful of ships that survived could barely manage their rendevous with the Point K forward base.

One confirmed survivor was Lt. Commander Scott Bernard, who safely landed somewhere in Central America. As he grieved over the loss of his fiancé, Marlene Rush, he had one objective in mind - eliminate Reflex Point. Realizing his Alpha Fighter was completely unusable, he donned his armor and rode off on his emergency Cyclone armor towards his destination. In his journey to Reflex Point, he meets Rand, a drifter of the wastelands. The two share a strange bond, and continue on into the unknown. Along the way, they encounter Lance "Lancer" Belmont, under the guide of Yellow Dancer. He joins Scott's resistance cell, thinking he might be his best hope at finally making a real difference in his underground war with the Invid. In no time, others members began joining Scott's rag-tag group, such as the vigilante Rook Bartley, the marriage-obsessed Annie, the bioengineer Lunk (who happened to have a spare Alpha Fighter with him at the time).

As Scott's assembled resistance fighters fight their way through Invid infested territory of Northern Brazil, they encounter a variety of colorful characters, including Jonathan Wolfe, a war hero of the REF. Wolfe had become the leader of Soldiertown, an alleged safe haven for military troops and milita from Invid forces. Scott, having been originally part of Wolfe's squadron, the Wolf Pack years before, is more than a little beside himself when he meets the famous veteran. He agrees to join him in a mission to assault an Invid Hive nearby. Rand, a little more than suspicious of the city's lackadaisy attitude towards the enemy, confronts Wolfe after he sees him making a Protoculture Cell exhange with the Invid. It turns out that Wolfe had been exchanging soldiers' lives for a steady supply of Protoculture. Wolfe, who had been on Earth since coming back from deep space to fight the Robotech Masters, has grown numb to tragedy and weary of war. He has a change of heart as he sees young Scott Bernard, who reminded him of when he was a young officer, fighting for his life against Invid Shock Troopers. Wolfe jumps aboard his Alpha and saves the day, but at the cost of his life. As he lay dying, he cries out for his son, Johnny, and his wife. Scott Bernard then salutes the fallen hero.

As Scott and his group leave to head to Point K, the Invid Regess, amused that her experiment failed, prepares an invasion force to wipe out Soldiertown.

Soon, Scott arrives at the ruins of Point K. As the fog clears, he is shocked to find out that such a massive forward base could be destroyed. Realizing the foolishness of his goal to destroy Reflex Point, he falls into a deep depression. His friends try to cheer him up to no avail. Rand and Rook split up, only to stumble upon a ruined village that was caught in the fighting. There they find the mysterious amnesiac survivor, whom the group later names Marlene. Unbeknownst to the group at the time, Marlene was secretly an Invid stimulagent and an important figure in the Invid heirarchy. As the Invid approach the freedom fighters, Marlene begins acting like a crazy woman. Scott sees her cries for help, and is somehow reminded of his own fiance, Marlene Rush's violent death at the hands of the Invid. Scott charges to his Alpha and rushes to confront the enemy. Scott, his fighting spirit renewed, rallies his friends and proceeds to their destination of Reflex Point.

The group gets into several more misadventures along the way. They take out an Invid fortress on the mountains, Lancer meets a figure from his past, Carla, has shacked up with an amoral, corrupt major. The group then commandeer a boat from a long-abandoned Southern Cross naval facility to sail to North America. One night, Rand has visions as he inhales the spores of the Flower of Life. They face dinosaurs in the Invid Regess' evolutionary experiment site, the Genesis Pits, and along with a handful of war-weary veterans, take out an Invid Broadcast Tower. The group take a breather on the long lost city of Denver, abandoned since the end of the Second Robotech War. Finally, they encounter Corg, another Invid that has been transmogrified into human form by the Regess, as he begins a genocidal rampage in New York City. In the meantime, Scott begins to fall Marlene, while Lancer becomes involved with another Invid stimulagent, Sera.

Roughly a year after the disastrous failure of the Second Reclamation Force, a new full-scale assault was ordered by Admiral Rick Hunter. After receving approval from the governing council, the bulk of Mars Base' forces ready themselves to against Reflex Point, and rid the galaxy of the Invid Regess once and for all. An earlier battalion from Jupiter Section was sent in, under the command of Sue Graham, who failed to report back her report on the Invid's current strength.

The REF briefly delay the attack when the Super Dimension Fortress Three (SDF 3) and its support cruisers fail to defold. General Reinhardt has no choice and assumes full command of the assembled fleets and begins the final battle against the Invid for control of Earth. The fleet moves into position.

The bulk of the REF fleet defolds near Earth. Admiral Hunter is nowhere to be seen.

Initially, the final battle of the Third Robotech War proceeded well for the REF. The capital ships' massive Synchro Cannons knock out a number of Invid carriers before they could launch their entire complement of Invid troopers. The use of Shadow Technology this enabled REF fighters to evade detection by the Invid forces. the first Invid attack wave from the Northern Hemisphere was defeated. On the ground, resistance forces, assisted by REF commandos, fight their way to Reflex Point. Scott's own rag-tag group of freedom fighters charge through the battlefield. Marlene, having regained her identity as the Invid princess Ariel, leads them within the Main Hive's innermost sanctum.

The Regess could scarcely believe her own daughter had betrayed her own race, and tells her that she intends to fight to the bitter end. She launches a second assault wave composed of most her remaining forces on Earth. Every available Invid fighter on the planet is sent into orbit, while all Invid ground troops are pulled back to defend Reflex Point. As the fighting intensified, the Invid forces in space soon greatly outnumbered the terran fighters, and begin taking heavy losses. In a matter of moments, they punch through the REF's front lines, much to the dismay of General Reinhardt and his command crew, who could only stare from a distance onboard their ship. Hundreds die as the Invid begin resorting to suicide runs against the REF capital ships. Meanwhile, the Terran ground forces also found themselves in an equally hopeless situation against the relentless Invid forces.

The Regess confronts the freedom fighters.

General Reinhardt, with previous approval from Admiral Rick Hunter, decides that rather than lose their entire fleet, he must launch the world-destroying Neutron-S Missiles on Earth.

The Invid Regess sees this and is dismayed at the lengths humanity would take to destroy her entire race. Between Sera and Ariel, Lancer, Annie, Lunk and the rest of the resistance group arguing with her to spare the planet, and the incoming missiles, she realized she had had enough. Already, she could hear another world calling out to her - one that might be less problematic than the one she's currently occupying. The Regess calls out to her entire civilization and begins her exodus from Earth.

The Invid Regess, as a parting gift to her daughters Ariel andSera, both of whom had chosen to stay on Earth, destroys the Neutron-S Missiles (as well as a few unlucky REF vessels) as she makes her way to the cosmos. The Third Robotech War is finally over.

Although victorious, the expeditionary forces suffered significant losses at the hands of the Invid. The mystery regarding Admiral Rick Hunter and his ship's disappearance would perplex many for some time to come. Earth finally feels secure and renewed, Yellow Dancer holds a farewell concert where he finally reveals himself to be Lancer. Scott, Ariel, Rand, Rook, Annie, Lunk and Sera could only watch in amusement as the audience stares dumbfounded. The group share a few moment together, recounting their experiences with one another. Soon, the group disbands. Scott promises Ariel he'll return after he finds the missing SDF-3. He climbs aboard his newly-repaired Alpha-Beta Fighter, and says farewell to his comrades with a formal salute. Scott lifts off, with Ariel wondering if he'll keep his promise. Rook and Rand head off into the sunset together to begin a new adventure, while Lancer and Sera seek to find a new peaceful life together. Lunk and Annie have become close, he offers to watch over her, they decide to start a farm in the countryside and ask Ariel to join them until Scott returns. While much of Earth has been blown back to the Stone Age, there remains hope that society can begin rebuilding itself once again.